Much has been written about the biological mechanisms that result in nucleotide substitution processes being strand asymmetric and there is now substantial empirical evidence to support strand asymmetry's existence in nature. [1]} provide a good review of the subject. Strand asymmetry seems to be a localised phenomenon, existing on the scale of genes rather than genomes, and appears to be common in prokaryote and organelle genomes but not in eukaryotes. Nucleotide compositional asymmetry is the most common measure used for statistical inference. Under very loose assumptions [2]}, [3]} a strand-symmetric process should result in the proportions of As and Ts being equal and the proportions of Gs and Cs being equal on a single strand. Strand asymmetry can also be inferred by directly comparing estimated rates of nucleotide substitution, although most of the evidence seems to come from counting substitutions in ancestral state reconstructions based on maximum parsimony [4]}, [5]}, [6]}.
